In logs it usually prints CPU usage exceed messages, at times it have cross 90%

I wanted to know how does it calculate the CPU usage, its obvious that server contains multiple CPU therefore the messages printed in the logs are combine of all the CPU or does it calculate individually ?

Veritas Cluster Server (VCS) use kstat on Solaris to calculate CPU usage within code. But you could use mpstat to check and compare with the value from VCS HostMonitor agent.

Basically the CPU usage reported by HostMonitor agent is an average value over the MonitorInterval period of the usage of all CPUs. So the value is a average value during the last period of MonitorInterval secs, and combined all CPUs usage.